Protein target profile
VK055_1195
indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase
Strong target candidate with converging metabolic, structural and chemical evidence.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Evidence coverage
Terms and data sources used on this page
PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.
AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.
ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.
pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.
FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.
Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.
PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.
ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.
ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.
LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.
Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.
DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.
Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.
EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.
KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.
Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.
Prioritization evidence
Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.
Off-target risk
- Human off-target
- No hit
- Gut microbiome similarity
- 3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 46.222 Higher values support similarity to known essential genes.
Localization
- Localization
- Cytoplasmic
Structure confidence
- ColabFold pLDDT
- 96.72 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelThe selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.
Sequence
Sequence
Primary amino-acid sequence viewer.
MQTVLAKIVADKAIWVEARKQQQPLASFQNEIVPTQRNFYDALAGTRTTFILECKKASPSKGLIREDFDPAAIASIYKHYASAISVLCDEKYFQGSFDFLPIVSQVAPQPILCKDFTIDPYQIYLARYYQADACLLMLSVLDDEQYRQLSAVAHSLNMGVLTEVSNEEELERAIALKAKVVGINNRDLRDMSIDLNRTRQLAARLGPDVTVISESGIHTYAEVRELSHFANGFLIGSALMEQADLEAAVKRVLLGENKVCGLTRPQDAQVAWESGAIYGGLIFVPTSPRAVNDAQAKAVIAAAPLQYVGVFRNAPLEEVVARAQALGLAAVQLHGDEDQAYIDALRDALADNVRIWKALSVGETFPARTLRHVDKYLLDNGQGGSGQRFDWSLLQGQDLRNVMLAGGLGADNCVEAAKSGCAGLDFNSGVESQPGIKDASKLASVFQTLRAY
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
4- GO:0004425 Catalysis of the reaction: 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate = 1-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O.
- GO:0004640 Catalysis of the reaction: N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate.
- GO:0006568 The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
- GO:0000162 The chemical reactions and pathways resulting in the formation of L-tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; L-tryptophan is synthesized from chorismate via anthranilate.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 2 | 260 | PANTHER | PTHR22854 | TRYPTOPHAN BIOSYNTHESIS PROTEIN |
| 2 | 260 | InterPro | IPR045186 | Indole-3-glycerol phosphate synthase |
| 257 | 450 | SUPERFAMILY | SSF51366 | Ribulose-phoshate binding barrel |
| 257 | 450 | InterPro | IPR011060 | Ribulose-phosphate binding barrel |
| 257 | 447 | Pfam | PF00697 | N-(5'phosphoribosyl)anthranilate (PRA) isomerase |
| 257 | 447 | InterPro | IPR001240 | N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain |
| 259 | 446 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I |
| 259 | 446 | InterPro | IPR013785 | Aldolase-type TIM barrel |
| 5 | 251 | Pfam | PF00218 | Indole-3-glycerol phosphate synthase |
| 5 | 251 | InterPro | IPR013798 | Indole-3-glycerol phosphate synthase domain |
| 50 | 68 | ProSitePatterns | PS00614 | Indole-3-glycerol phosphate synthase signature. |
| 50 | 68 | InterPro | IPR001468 | Indole-3-glycerol phosphate synthase, conserved site |
| 257 | 447 | CDD | cd00405 | PRAI |
| 255 | 452 | Hamap | MF_00135 | N-(5'-phosphoribosyl)anthranilate isomerase [trpF]. |
| 255 | 452 | InterPro | IPR001240 | N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain |
| 1 | 258 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I |
| 1 | 258 | InterPro | IPR013785 | Aldolase-type TIM barrel |
| 259 | 446 | FunFam | G3DSA:3.20.20.70:FF:000165 | Multifunctional fusion protein |
| 3 | 254 | Hamap | MF_00134_B | Indole-3-glycerol phosphate synthase [trpC]. |
| 3 | 254 | InterPro | IPR013798 | Indole-3-glycerol phosphate synthase domain |
| 1 | 251 | SUPERFAMILY | SSF51366 | Ribulose-phoshate binding barrel |
| 1 | 251 | InterPro | IPR011060 | Ribulose-phosphate binding barrel |
| 39 | 252 | CDD | cd00331 | IGPS |
| 39 | 252 | InterPro | IPR013798 | Indole-3-glycerol phosphate synthase domain |
| 1 | 256 | FunFam | G3DSA:3.20.20.70:FF:000024 | Indole-3-glycerol phosphate synthase |
3D structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
All structural evidence
Structural evidence
0 + 2Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold DB
AF_A0A0H3GW36
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_1195
|
ColabFold | — | — | full sequence | — | Loaded |
Ligand evidence
Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| 137 RCSB PDB | P00909 | 351.2 Da LogP -1.01 TPSA 176.8 | 1 viol. | ✓ Clean |
c1ccc(c(c1)C(=O)O)NC[C@H]([C@@H]([C@@H](COP(=O)…
|
|
| 3RG RCSB PDB | P9WFX7 | 195.2 Da LogP 0.88 TPSA 86.6 | ✓ Ro5 | ✓ Clean |
c1ccc(c(c1)C(=O)O)NCC(=O)O
|
|
| 4RG RCSB PDB | P9WFX7 | 228.2 Da LogP 2.96 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
c1ccc(cc1)OCc2cccc(c2)C(=O)O
|
|
| 5RG RCSB PDB | P9WFX7 | 155.1 Da LogP 1.11 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
c1cc(c(cc1F)C(=O)O)N
|
|
| BE2 RCSB PDB | P9WFX7 | 137.1 Da LogP 0.97 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
c1ccc(c(c1)C(=O)O)N
|
|
| BTB RCSB PDB | P9WFX7 | 209.2 Da LogP -3.01 TPSA 104.4 | ✓ Ro5 | ✓ Clean |
C(CO)N(CCO)C(CO)(CO)CO
|
|
| IGP RCSB PDB | P9WFX7 | 287.2 Da LogP 0.67 TPSA 123.0 | ✓ Ro5 | ✓ Clean |
c1ccc2c(c1)c(c[nH]2)[C@@H]([C@@H](COP(=O)(O)O)O…
|
|
| MLI RCSB PDB | P9WFX7 | 102.0 Da LogP -3.12 TPSA 80.3 | ✓ Ro5 | ✓ Clean |
C(C(=O)[O-])C(=O)[O-]
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC1615342 ZINC | 1.000 | 209.2 Da LogP -3.01 TPSA 104.4 | ✓ Ro5 | ✓ Clean |
OCCN(CCO)C(CO)(CO)CO
|
| ZINC3159089 ZINC | 1.000 | 228.2 Da LogP 2.96 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2ccccc2)c1
|
| ZINC1748751 ZINC | 0.813 | 228.2 Da LogP 2.96 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(OCc2ccccc2)c1
|
| ZINC2521416 ZINC | 0.771 | 258.3 Da LogP 2.97 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
COc1ccc(OCc2cccc(C(=O)O)c2)cc1
|
| ZINC2521429 ZINC | 0.771 | 246.2 Da LogP 3.10 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2ccc(F)cc2)c1
|
| ZINC2836260 ZINC | 0.771 | 354.1 Da LogP 3.57 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2ccc(I)cc2)c1
|
| ZINC356118 ZINC | 0.771 | 307.1 Da LogP 3.73 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2ccc(Br)cc2)c1
|
| ZINC466552 ZINC | 0.771 | 272.3 Da LogP 3.36 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
CCOc1ccc(OCc2cccc(C(=O)O)c2)cc1
|
| ZINC4746517 ZINC | 0.771 | 258.3 Da LogP 2.46 TPSA 66.8 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2ccc(CO)cc2)c1
|
| ZINC548897 ZINC | 0.771 | 262.7 Da LogP 3.62 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2ccc(Cl)cc2)c1
|
| ZINC19519722 ZINC | 0.750 | 271.3 Da LogP 2.06 TPSA 89.6 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ccc(OCc2cccc(C(=O)O)c2)cc1
|
| ZINC19808090 ZINC | 0.750 | 246.2 Da LogP 3.10 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2cccc(F)c2)c1
|
| ZINC2578413 ZINC | 0.750 | 307.1 Da LogP 3.73 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2cccc(Br)c2)c1
|
| ZINC2578450 ZINC | 0.750 | 284.4 Da LogP 4.26 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
CC(C)(C)c1ccc(OCc2cccc(C(=O)O)c2)cc1
|
| ZINC2578451 ZINC | 0.750 | 258.3 Da LogP 2.97 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
COc1cccc(OCc2cccc(C(=O)O)c2)c1
|
| ZINC32314 ZINC | 0.750 | 241.2 Da LogP 2.20 TPSA 80.4 | ✓ Ro5 | Alert |
Nc1ccccc1C(=O)c1ccccc1C(=O)O
|
| ZINC356120 ZINC | 0.750 | 278.3 Da LogP 4.12 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2ccc3ccccc3c2)c1
|
| ZINC4294630 ZINC | 0.750 | 262.7 Da LogP 3.62 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2cccc(Cl)c2)c1
|
| ZINC466629 ZINC | 0.750 | 256.3 Da LogP 3.53 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
CCc1ccc(OCc2cccc(C(=O)O)c2)cc1
|
| ZINC8729636 ZINC | 0.750 | 242.3 Da LogP 3.27 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
Cc1cccc(OCc2cccc(C(=O)O)c2)c1
|
| ZINC19434922 ZINC | 0.737 | 253.3 Da LogP 2.84 TPSA 70.3 | ✓ Ro5 | ✓ Clean |
N#Cc1cccc(OCc2cccc(C(=O)O)c2)c1
|
| ZINC19802919 ZINC | 0.730 | 253.3 Da LogP 2.84 TPSA 70.3 | ✓ Ro5 | ✓ Clean |
N#Cc1ccc(OCc2cccc(C(=O)O)c2)cc1
|
| ZINC2597425 ZINC | 0.730 | 256.3 Da LogP 2.78 TPSA 63.6 | ✓ Ro5 | ✓ Clean |
O=Cc1ccc(OCc2cccc(C(=O)O)c2)cc1
|
| ZINC16946859 ZINC | 0.722 | 304.3 Da LogP 4.63 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(-c2cccc(OCc3ccccc3)c2)c1
|
| ZINC203307995 ZINC | 0.722 | 242.3 Da LogP 3.05 TPSA 35.5 | ✓ Ro5 | ✓ Clean |
COC(=O)c1cccc(COc2ccccc2)c1
|
| ZINC8729642 ZINC | 0.722 | 256.3 Da LogP 3.58 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
Cc1cc(C)cc(OCc2cccc(C(=O)O)c2)c1
|
| ZINC2576716 ZINC | 0.711 | 270.3 Da LogP 4.09 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
CC(C)c1ccc(OCc2cccc(C(=O)O)c2)cc1
|
| ZINC37466450 ZINC | 0.711 | 256.3 Da LogP 2.78 TPSA 63.6 | ✓ Ro5 | ✓ Clean |
O=Cc1cccc(OCc2cccc(C(=O)O)c2)c1
|
| ZINC11802632 ZINC | 0.703 | 242.3 Da LogP 3.27 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
Cc1cccc(COc2cccc(C(=O)O)c2)c1
|
| ZINC13419082 ZINC | 0.703 | 307.1 Da LogP 3.73 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(OCc2cccc(Br)c2)c1
|
| ZINC16946848 ZINC | 0.703 | 304.3 Da LogP 4.63 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(-c2ccc(OCc3ccccc3)cc2)c1
|
| ZINC4943981 ZINC | 0.703 | 246.2 Da LogP 3.10 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(OCc2cccc(F)c2)c1
|
| ZINC7603991 ZINC | 0.703 | 262.7 Da LogP 3.62 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(OCc2cccc(Cl)c2)c1
|
| ZINC1532902 ZINC | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC2018106 ZINC | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@](O)(CC(=O)O)C(=O)O
|
| ZINC19472717 ZINC | 0.697 | 242.3 Da LogP 3.10 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COCc2ccccc2)c1
|
| ZINC2521417 ZINC | 0.692 | 273.2 Da LogP 2.87 TPSA 89.7 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2ccc([N+](=O)[O-])cc2)c1
|
| ZINC269415 ZINC | 0.690 | 215.2 Da LogP 2.64 TPSA 43.1 | ✓ Ro5 | Alert |
Nc1ccc(F)cc1C(=O)c1ccccc1
|
| ZINC19479622 ZINC | 0.686 | 226.3 Da LogP 2.55 TPSA 59.1 | ✓ Ro5 | ✓ Clean |
N=C(N)c1cccc(COc2ccccc2)c1
|
| ZINC5162233 ZINC | 0.682 | 212.3 Da LogP 2.08 TPSA 69.1 | ✓ Ro5 | Alert |
Nc1ccccc1C(=O)c1ccccc1N
|
| ZINC40564460 ZINC | 0.680 | 216.0 Da LogP 1.73 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
Nc1cccc(C(=O)O)c1Br
|
| ZINC22263788 ZINC | 0.675 | 298.3 Da LogP 3.49 TPSA 63.6 | ✓ Ro5 | ✓ Clean |
CC(=O)CCc1ccc(OCc2cccc(C(=O)O)c2)cc1
|
| ZINC37369446 ZINC | 0.675 | 306.3 Da LogP 2.37 TPSA 80.7 | ✓ Ro5 | ✓ Clean |
CS(=O)(=O)c1cccc(OCc2cccc(C(=O)O)c2)c1
|
| ZINC13080039 ZINC | 0.667 | 296.2 Da LogP 3.98 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(OCc2cccc(C(F)(F)F)c2)c1
|
| ZINC166323 ZINC | 0.667 | 228.2 Da LogP 2.96 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(COc2ccccc2)cc1
|
| ZINC169677 ZINC | 0.667 | 228.2 Da LogP 2.96 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(OCc2ccccc2)cc1
|
| ZINC2512344 ZINC | 0.667 | 219.0 Da LogP 2.29 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cc(F)ccc1Br
|
| ZINC2578452 ZINC | 0.658 | 307.1 Da LogP 3.73 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2ccccc2Br)c1
|
| ZINC280728 ZINC | 0.658 | 262.7 Da LogP 3.62 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(COc2ccccc2Cl)c1
|
| ZINC465988 ZINC | 0.658 | 258.3 Da LogP 2.97 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
COc1ccccc1OCc1cccc(C(=O)O)c1
|
PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.